Dendrix

Dendrix (De novo Driver Ex Exclusivity) is an algorithm that identifies driver groups of mutations without prior information, using the exclusivity property observed for mutations in a driver pathway.

 

People (strict random order): Fabio Vandin, Hsin-Ta Wu, Eli Upfal, Ben Raphael.

 

references

The Dendrix algorithm is described in the following publications:

  • F. Vandin, E. Upfal, and B.J. Raphael. (2011) De Novo Discovery of Mutated Driver Pathways in Cancer. (Abstract) Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2011), pag:499-500.
  • F. Vandin, E. Upfal, and B.J. Raphael. De novo discovery of mutated driver pathways in cancer. Genome Research (2011) Jul 11. [Epub ahead of print]

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    download

    Beta version of Dendrix is available.

  • Dendrix (ver0.3, February 4, 2013): for finding significant groups of mutations (with collapsing level -gene, protein domain, etc.- for mutations defined by the user) based on coverage and exclusivity in the alteration matrix.
  • contact: dendrix@cs.brown.edu

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    requirements

  • Python

    • how-to

    Detailed instructions for running Dendrix are provided in the README.txt file in the release above.

     

    visualization

    Cytoscape plugin: visualize the result of Dendrix.